[English] 日本語
Yorodumi
- PDB-7uba: Structure of fungal Hop1 CBR domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7uba
TitleStructure of fungal Hop1 CBR domain
ComponentsHORMA domain-containing protein
KeywordsDNA BINDING PROTEIN / meiosis / HORMAD / PHD / winged helix
Function / homologyHORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / HORMA domain-containing protein
Function and homology information
Biological speciesVanderwaltozyma polyspora DSM 70294 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.599 Å
AuthorsUr, S.N. / Corbett, K.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM104141 United States
CitationJournal: EMBO J / Year: 2024
Title: Chromatin binding by HORMAD proteins regulates meiotic recombination initiation.
Authors: Carolyn R Milano / Sarah N Ur / Yajie Gu / Jessie Zhang / Rachal Allison / George Brown / Matthew J Neale / Eelco C Tromer / Kevin D Corbett / Andreas Hochwagen /
Abstract: The meiotic chromosome axis coordinates chromosome organization and interhomolog recombination in meiotic prophase and is essential for fertility. In S. cerevisiae, the HORMAD protein Hop1 mediates ...The meiotic chromosome axis coordinates chromosome organization and interhomolog recombination in meiotic prophase and is essential for fertility. In S. cerevisiae, the HORMAD protein Hop1 mediates the enrichment of axis proteins at nucleosome-rich islands through a central chromatin-binding region (CBR). Here, we use cryoelectron microscopy to show that the Hop1 CBR directly recognizes bent nucleosomal DNA through a composite interface in its PHD and winged helix-turn-helix domains. Targeted disruption of the Hop1 CBR-nucleosome interface causes a localized reduction of axis protein binding and meiotic DNA double-strand breaks (DSBs) in axis islands and leads to defects in chromosome synapsis. Synthetic effects with mutants of the Hop1 regulator Pch2 suggest that nucleosome binding delays a conformational switch in Hop1 from a DSB-promoting, Pch2-inaccessible state to a DSB-inactive, Pch2-accessible state to regulate the extent of meiotic DSB formation. Phylogenetic analyses of meiotic HORMADs reveal an ancient origin of the CBR, suggesting that the mechanisms we uncover are broadly conserved.
History
DepositionMar 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HORMA domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9976
Polymers24,2391
Non-polymers7595
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.389, 38.917, 68.981
Angle α, β, γ (deg.)90.000, 109.040, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein HORMA domain-containing protein


Mass: 24238.605 Da / Num. of mol.: 1 / Fragment: residues 317-529
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vanderwaltozyma polyspora DSM 70294 (fungus)
Strain: ATCC 22028 / DSM 70294 / BCRC 21397 / CBS 2163 / NBRC 10782 / NRRL Y-8283 / UCD 57-17
Gene: Kpol_411p8 / Production host: Escherichia coli (E. coli) / References: UniProt: A7TRP1

-
Non-polymers , 5 types, 216 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.5, 30% PEG 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.283 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283 Å / Relative weight: 1
ReflectionResolution: 1.51→32.6 Å / Num. obs: 65701 / % possible obs: 98.5 % / Redundancy: 3.34 % / Biso Wilson estimate: 20.07 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.057 / Net I/σ(I): 13.93
Reflection shellResolution: 1.51→1.61 Å / Redundancy: 1.97 % / Num. unique obs: 7028 / CC1/2: 0.53 / Rrim(I) all: 0.804 / % possible all: 61

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.599→32.6 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0.35 / Phase error: 15.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1635 4357 7.32 %
Rwork0.1436 55192 -
obs0.1451 59549 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.5 Å2 / Biso mean: 28.0981 Å2 / Biso min: 10.43 Å2
Refinement stepCycle: final / Resolution: 1.599→32.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1492 0 1131 211 2834
Biso mean--33.56 37.07 -
Num. residues----122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011560
X-RAY DIFFRACTIONf_angle_d1.3092083
X-RAY DIFFRACTIONf_chiral_restr0.053219
X-RAY DIFFRACTIONf_plane_restr0.007265
X-RAY DIFFRACTIONf_dihedral_angle_d16.549613
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.599-1.61670.25921110.2343153082
1.6167-1.63570.23761110.2245167589
1.6357-1.65570.2411490.2108178595
1.6557-1.67660.24481290.1901183298
1.6766-1.69870.20691630.1781854100
1.6987-1.72190.18141490.16471873100
1.7219-1.74650.18251370.15371809100
1.7465-1.77260.17361520.15971913100
1.7726-1.80030.19681400.14761839100
1.8003-1.82980.18141460.14521919100
1.8298-1.86140.16471510.14391859100
1.8614-1.89520.15861640.13611819100
1.8952-1.93170.1651530.15311897100
1.9317-1.97110.1911380.1431847100
1.9711-2.01390.17341420.14731855100
2.0139-2.06080.16571480.13311848100
2.0608-2.11230.1451460.13251858100
2.1123-2.16940.14861480.13511886100
2.1694-2.23320.15211500.1271860100
2.2332-2.30530.17611460.12951869100
2.3053-2.38770.15051520.12361836100
2.3877-2.48320.16391460.13191861100
2.4832-2.59620.16321440.13021878100
2.5962-2.7330.16781520.13761876100
2.733-2.90410.16541440.15581842100
2.9041-3.12820.14841520.14381852100
3.1282-3.44270.16571450.14951861100
3.4427-3.94010.15261490.1368186699
3.9401-4.96130.14291500.12431857100
4.9613-32.60.15851500.1633183699
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7211-0.301-0.69152.1072-0.14462.2032-0.0012-0.07710.00140.0174-0.0337-0.1629-0.0460.10130.0070.1125-0.0005-0.0030.0956-0.00590.1379.6855-2.3812-27.7881
21.36160.1369-1.0280.9713-0.20392.4865-0.0108-0.22230.03060.20310.0166-0.0402-0.09230.02880.02190.1410.0026-0.020.1568-0.01420.12840.6195-0.3597-17.4342
31.7976-0.69360.05861.1712-0.41762.3221-0.199-0.4764-0.29810.29640.07110.11750.2888-0.40120.02810.2263-0.01930.03740.31680.06030.2397-9.6881-10.1373-8.9755
41.9905-0.1653-0.33821.5719-0.19822.8781-0.0087-0.00810.1283-0.0062-0.01710.1728-0.1389-0.3440.00910.12820.0204-0.02530.2017-0.00830.1803-8.51732.5721-26.9346
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resi 319:361A319 - 440
2X-RAY DIFFRACTION2chain A and resi 362:428A319 - 440
3X-RAY DIFFRACTION3chain A and resi 429:497A319 - 440
4X-RAY DIFFRACTION4chain A and resi 498:524A319 - 440

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more